The Last Replicator
by 10000 SGA Fans can't be wrong
Summary: What if Elizabeth and the other Replicators had decided to stay in Atlantis to create their human bodies instead of leaving at the end of “Ghost in the Machine?” How would the season then turn out? Full summary inside. R@R, Please! AU.
1. Chapter 1

Disclaimer: I don't own Stargate: Atlantis. If I did, it wouldn't be cancelled at the end of this season.

Summary: What if Elizabeth and the other Replicators had decided to stay in Atlantis to create their human bodies instead of leaving at the end of "Ghost in the Machine?" How would the season then turn out? With Michael gathering his forces, Todd coming up with a surprising solution to the problem of the remaining Wraith (minus his hive, of course), and a surprising lab in the city concerning biological weapons against the Wraith, Sheppard and company will be have to keep ahead of everything or be left behind in the new order of the Pegasus Galaxy. AU.

It was later, back in Woolsey's office. John and Elizabeth had hurried back after the destruction of Koracen to find all of the other Replicators sitting sedately in the work room they had set up. Most were shocked, and some were miserable about the accident; mostly because Koracen had set this all up and broke the Lantean's trust, some because of the results of the plot. Koracen had been well liked by some of the surviving Replicators.

"So what now, Elizabeth? Do you want to stay and keep working, or do you want to leave?" That was Woolsey, who had been ready to ship all the rest of the machines home after he learned of the double-cross, but once John and Elizabeth had told him of Koracen's fate, he calmed down. Particularly when he saw that several of the others had gone back to working on the machines to build human bodies. Going straight back to work with no further interruptions impressed him.

"I think that we should leave. If Koracen could betray us, so could any of the others. IT's too risky."

Woolsey made a face. "To be perfectly honest with you, I don't see much problem with the others. They just went straight back to work, and have almost completed the mind transfer device, as Doctor McKay has informed me."

Elizabeth smiled briefly. "And how long did he take to inform you?"

Woolsey rolled his eyes. "About fifteen minutes. Between complimenting the efficiency of Replicator workers and whining about how it was too bad humans weren't like that, he barely had time to say what he originally tried to tell me."

"I guess some things never change. Did I ever tell you about the time he sent me thirty-something emails about why we should have kept another Z.P.M on Atlantis instead of sending it back to Earth?"

"I'll bet that was fun."

"Not really. But as you were saying; yes, we have made some progress, but we still are a major security breach." Here, Elizabeth cast a nervous glance at John. Woolsey turned to him also. Rodney, Ronon, and Teyla walked up then and started staring at John as well. Now John became nervous. "What?"

Woolsey adopted his "answer-me-now" face. "Colonel Sheppard, you are the ranking military officer on this base. You have a say in this, too. Right now, if you say it's too dangerous, then they would probably leave, with or without asking."

Elizabeth broke in with "John, I know you don't trust me, but please believe me when I say that we are not your enemies. Just give us another chance."

Rodney probably then made up John's headache from being thrown into a wall by Koracen come back when he popped up with "Come on, John, if it works, then they'll be the same as us. Would you trust them more if they were human?"

John was starting to feel overwhelmed when Teyla said "I agree with Rodney. Also, I believe that this is truly Elizabeth, and that she is our ally."

The Colonel had pretty much made up his mind, but he needed one more opinion. "Ronon, how 'bout you? What do you think?

Ronon glared at the Replicators that were standing below in the Gate Room. They're Replicators, Sheppard. I don't trust 'em." Here, his face became a little softer, if possible. "But since Doctor Weir let me stay here when I found you guys, I'll give her another shot at it. I owe her that."

Elizabeth was surprised that Ronon would allow her this. She turned back to John to await his decision. Deep down, she hoped that John would let them stay, but the practical part of her nanites knew that that might be too much to hope for. She heard John take a deep breath and, despite what his team had said, braced herself for the worst.

"Okay. I'll let you guys stay."

Elizabeth started and looked up at him in hope. John raised a finger. "However, there will be some restrictions, like before." Elizabeth nodded eagerly. "There will be a number of forcefields around your lab, there will be guards with ARGs outside the lab at all times, and once the human bodies are completed, your machine bodies will be destroyed, so there's no way to go back. Agreed?

Elizabeth and Woolsey both nodded in agreement. "Agreed. We will not get in your way at all. However, once we are finished, what will you do with us then?"

Woolsey spoke up at this point. "At that point, I see no problem integrating you with the rest of the base- under guard for the first week or so, of course. If you want to leave or stay after that is your choice." The unspoken question hung in the air: _And what of you, Elizabeth? Will you stay with us or go with the others to ascend?_ However, the awkward moment was passed by as Elizabeth rose, saying: "I will discuss this with the others; it is their choice as well.

"Very well." Woolsey looked pleased.

In the end, the Replicators decided to stay. A few had voted against staying, obviously feeling uncomfortable around so many humans, as well as being under guard, but they were swayed by the others. They then headed back to their lab to try to complete the equipment needed.

John and the team stood with Woolsey in his office, watching the last of the Replicators get what they needed. Woolsey then turned to John and said quietly, "I hope you're right about this."

"Me too. At least Koracen's gone."

--Commercial break--

It was a week later, and everything was looking up. Most of the machines needed to build the new bodies were either completed or almost finished. Earlier in the week, John had spoken to the prophet- er, McKay, and asked for a timeframe. Rodney's response was positive. "Normally, with humans building this type of technology, it would take a hell of a lot longer time than it would for our guests. They don't need food, sleep, bathroom breaks, _and_ they know exactly what they are doing. The perfect workers. If only we could create more that could work for us…"

"Hey, careful, Rodney. Remember the Terminator movies."

"Ha-ha. Very funny. Now if you'll excuse me, I have a Z.P.M. to build."

"Really? Given up on recharging them like last time? Maybe you're growing some sense, after all. Just don't bring another parallel universe copy of yourself here again."

"Sheppard?"

"Yes?"

"Leave."

That was a while ago, and John was now roaming the city for something to fiddle around with. Normally, that was McKay's job, but they hadn't gone exploring for a while, and John was bored. He walked the city until he found that he was in a recently unflooded section of the city. They had never been this way, preferring to stay in safe territory.

John kept walking until he found a single door at the end of a hall. He went through, and had the shock of his life:

Wraith. Wraith bodies in stasis boxes around the wall. There were several computer panels on the walls, and some on pedestals in the center of the room. After a closer look, John realized the all of the Wraith were dead; all with various needle puncture marks and some with mutilated features. John grabbed his radio.

"This is Colonel Sheppard. Get Doctors McKay and Keller down to my location right now. I've found something they should see.

--Commercial break --

"It's a lab. A lab concerning biological weapons against the Wraith. Some were injections, some were bombs. Any way they did it, however, it didn't work." That was McKay after a very thorough investigation.

"Why didn't it work?" Woolsey asked. He had been shocked when he entered the lab and saw all of the Wraith bodies.

Keller stepped in at that point. "It was actually based on a Lantean version of Carson Beckett's retrovirus. The drug or gas would tear away the iratus bug genes in the Wraith, destroy them, and then actually deteriorate the human cells until they died. That was the original idea, and it worked well in injections, but the gas form didn't exactly work as well."

"And why not? From what I can tell, there seems to be no problem."

Jennifer turned a little green when she voiced her response: "The problem was that any humans or Ancients caught in the blast would suffer the same fate as the Wraith. When you think about it, it's almost the same as the Wraith feeding process, without the draining of the life force: age the cells, and the victim dies. Apparently some Ancient had a twisted sense of humor; kill the Wraith with their own feeding technique."

Woolsey also turned a little green. "That is… disturbing. Is there any way you could make the bomb so that it only affected Wraith?"

"Well, one way would be to beam it onto a Wraith ship, and then hightail our asses out of there." John helpfully put in. Ronon, behind him, grinned appreciatively.

Rodney clicked his fingers at John. "Uh, Colonel, remember? E.M. field around all Wraith ships? No beaming in or out?"

John shrugged. "Maybe we can get the Replicators to help us."

McKay was about to reply when a lieutenant came through the doorway, saluted, and then addressed Mr. Woolsey and John: "Sir? I got a message from the Replicators? They've finished all their equipment and want you to know they're almost done. Apparently, they'd like you to be there when the bodies are built."

John nodded. "Thanks, Lieutenant." The man nodded and walked away. He turned to Woolsey and the team. "Well, guys, let's go watch some machines build humans. He walked out the door, hearing McKay's parting shot: "Machines building humans? Sounds like a Terminator movie in reverse! Movie freak."

John chuckled.

A.N. Phew! That took a while to write. I've had this story idea bouncing around my head for a couple weeks, and have decided to finally put it down on paper- figuratively, of course. Anyway, I've got a question for you to put in your _**review**_: Should Elizabeth get her new body to look like her old body, or should she stick with FRAN's image? I'm leaning toward her keeping FRAN's image, myself. And of course, please review or I'll send Michael after you and turn you into a hive ship. That's a promise.  Bye!


	2. Chapter 2

A.N. Wow, six reviews overnight. Keep it up, people! Remember, the more reviews I get, the more inclined I am to write every day.

This chapter starts off when the Replicators are transferring into human bodies. Just so you know.

_Chapter 2:_

Everything was going according to plan so far. The machines were built, several human bodies were ready, and Woolsey, Sheppard, McKay, Ronon, and Teyla were outside the lab, watching on monitors. Teyla, who had been deep in thought on the way to the lab, spoke up. "John, if this all goes well, will Elizabeth go with the others, or…" She left the statement unfinished.

"Teyla, I sort of hope she'll stay, but she has an obligation to these people. She started all this, I think she'll want to complete it, too. That's what makes her Elizabeth."

Woolsey added his two cents in. "That's how Elizabeth always was. Whenever she had a job to do, she would do anything to see it through. But…" He trailed off, staring into space, as he usually did when he had ideas coming.

"But what?"

"This is the city of the Ancients, of course. What better or more fitting place for the Replicators to complete their work on ascension than in the home of the parents they were trying to emulate? Of course, if they don't feel comfortable here, we can always direct them to that one planet, um, um, M6R-something-something-something. You, know that planet where Colonel Sheppard stayed for a couple hours with those people trying to ascend?"

"Hey! Try six months!"

"Of course. Anyways, that planet is an option, too, correct?"

Ronon broke in. "Look. They're starting." He was right. The first human body was on the table, lying there without moving. "That's really weird. Looks like we've got a corpse on life support." That was McKay, and he was right. The body had an oxygen mask on, as well as blood pressure and heartbeat machines thoughtfully provided by Doctor Keller nearby. Elizabeth, inside the lab, turned toward the camera and spoke. "Alright, we're just about to start the first transfer. It should only take a few minutes, and when we're done, we will destroy our old bodies."

Woolsey nodded. "Just to be safe, I'd like Doctor McKay to be there to help with the scrapping of the machine bodies." Elizabeth flinched a little at the term 'scrapping', but agreed. Rodney, unable to contain himself, spoke up: "And when we're done, Elizabeth, if you don't mind, I'd like to get some advice on the building of Zed.P.Ms here. Zelenka and I just can't agree on certain points. And also, about getting more power to the city shields, with your input, I'd like-MMMPH!!" The 'MMMPH' was Ronon's hand clamping over Rodney's mouth. John clapped Ronon on the back in satisfaction. Elizabeth laughed.

"We'll begin now."

The process for the first few Replicators went smoothly enough. The first one- Lia, her name was- lay down on a worktable, had the mind transfer device attached to her, had the other Replicators type in some code, and relaxed. Next, there was a flash of light, and the human body suddenly was alive. The newly made human sat up in bewilderment, and then jumped up and hugged Elizabeth in delight. Every single Replicator-turned-human did the exact same thing, until it was Elizabeth's turn.

At first it went smoothly enough. The body looked the exact same as how she used to look, before she was captured. But, everything went wrong: Instead of the mind switching bodies like it was supposed to, the human body disintegrated, and the machine shut down. Elizabeth sat up, perplexed, and the new 

humans rushed over in concern. John was shocked. He turned to McKay. "What happened here, Rodney? What's going on?!"

Rodney was feverishly typing away at his computer. He looked up at John, his face in horror. "I can't be sure… but I think that the machine is rejecting Elizabeth's mind to that body in the transfer, and so is sending her back."

Woolsey stared. "Could it be a human- er, Replicator error?"

"Of _course_ not! The only way for something like this to happen would be if someone purposely sabotaged the machine to reject Elizabeth's mind to that body." He looked at Elizabeth, who had been listening to him through the glass. "Oh, no."

"What?"

Rodney spoke at the same time Elizabeth shouted out the name in fury: "_Koracen_!!"

That was five days ago, and once Elizabeth had calmed down after setting a new record for the number of swear words used in a sentence, she explained that the only way that this could work for her would be to either create a new body and image completely from scratch, or use F.R.A.Ns image for her human body. The quicker way was F.R.A.Ns image, which Mr. Woolsey decided was the option they would take. John and Rodney had protested- rather loudly- until Woolsey pointedly asked them if they would prefer Elizabeth having no human body. John sulked for a while after that. Elizabeth, however, was looking on the positive side.

"Think of it like this, John: Now I'm younger and better looking than ever. Also, if I had gotten my first body back, I'd have to answer a lot of questions, as I'm officially dead on Earth." After that little declaration, John calmed down.

The Asuran humans (A.N. that's how I'm going to refer to them from now on) were divided. One group felt like they should leave the city, as they thought the Earth humans still didn't trust them; and the other group wanted to stay and complete their work on ascension here. Elizabeth was undecided. Most of her wanted to stay, but a small part of her- the part that told her she should stay with the group – felt like they would work better somewhere else. The next morning, she walked to the Gate room and asked to see Mr. Woolsey.

"Doctor Weir, what can I do for you?"

"I've got a rather large dilemma, Mr. Woolsey., and I was hoping you could help with it. Of course, it would be your final decision anyway."

"Ah. You are referring to whether or not to stay in the city?" Elizabeth nodded. "Well, I have no problem with that, as long as there aren't any more 'incidents' like Koracen."

"Richard, I can promise you that that will not happen. After all, we're just like you now. We couldn't harm you if we tried."

"So does that mean you will stay? I'm sure that there are many people who missed you greatly." Mr. Woolsey remarked. He gave her a look. "Colonel Sheppard the most, probably."

Elizabeth turned so red that Mr. Woolsey picked up an apple and started comparing the colors of it and her face. "Hmm. Interesting."

After a couple moments, Elizabeth found her voice. "Sir, I don't know about _that_," Mr. Woolsey looked at her like _yeah, right_, "But I think we will stay."

Mr. Woolsey nodded. "Very well. I'll have quarters set up for all of you. There are nine of you, yes?" She nodded. "Excellent. Shall I set up yours as close to Colonel Sheppard as possible?"

"_Sir!_"

Woolsey chuckled.

John Sheppard was extremely tired. It had just been a day since Rodney had gotten that parasite in his brain. It took three weeks, and it finally turned out with Ronon being right about the Ancient device called the Shrine of Talus. That had given John a huge headache just being near that thing, and it hadn't gone away. He decided that if any more people got the same bug, he'd play sick.

It was 12:30 at night, and John was just about to go to bed when he heard a knock on his door; a soft knock this time. "Come in." The door opened and there was Rodney again, this time looking a little more relaxed. "What's up Rodney?"

"Well, I couldn't sleep again, and I felt like going to the East Pier again. Wanna come?"

"Sure. I'll get the beer.

"Right. I got the chocolate."

"You have chocolate? Didn't you lose that all on poker night to Lorne? Actually, don't you still owe Zelenka some?

"Yeah, well, still. I'll just say that I needed to bribe my niece and lost it all."

"Your head. At least I'll be free of suspicion. Come on, let's go."

However, when they got to the pier, they had a small surprise: Woolsey was out there with a can of beer and a pillow. "Sir, what are you doing here?"

"Oh, just thinking about what's been happening lately. Are all missions like this in the Pegasus Galaxy? Or is it just always weird here?"

"Probably both, Sir."

"Well, why don't you two take a seat? It's going to be a long night." He turned around and saw them. They also saw he was slightly drunk. "Oh, good, more beer. I've run out."

"I don't think you should have any more beer, sir. What's on your mind?"

"How about if I made the right decision with the Replicators in the city?"

"Well, they've been harmless so far."

"I suppose you're right. What about Elizabeth? Can we trust her? Should we?"

Rodney started talking at this point. "I'm sure they are perfectly harmless, Mr. Woolsey. All they want to do- or talk about- is ascension. A really boring topic."

"And Elizabeth? What will she do?" Rodney looked helplessly at John when Woolsey voiced the question, and John decided to take pity on him. "Sir, knowing her, she'll probably help all the others ascend and then stay with us." His voice trailed off. "At least, that's what I'm hoping." He muttered. He sat down with Woolsey and opened a can of beer. Rodney, still worried a little about Woolsey, sat down next to John and opened some of his chocolate and beer. They sat like that for a while, drinking beer and eating chocolate (turned out Woolsey had a not-so-small dark chocolate addiction), until John's radio beeped. "Go ahead."

"Sir, this is Captain Banks. There's a… weird energy reading coming from one of the guest's rooms. There are nine life signs there, and eight are slowly fading."

John looked over at Woolsey sharply, tiredness slipping away instantly. Woolsey however, was more than a little drunk. "Come on, Rodney, we gotta sober Woolsey up."

"How?"

"Follow me. Pick him up, careful." Together they carried Woolsey toward something that looked suspiciously like a boat ramp. John motioned to a deep part. "Over here, this looks good."

Rodney, catching on lifted Woolsey's legs up, pointing his head toward the water. Together, they careful lowered his head down, and then quickly dunked his head into the water. Woolsey came up spluttering. He was about to chew out John when Rodney forestalled him saying, "There's no time. The Asurans are ascending."

All conversation was put off while the three men dashed off towards the transporter.

When the men arrived in the quarters, there were eight almost ascended beings and one human watching them sadly. That one was Elizabeth. She turned toward them and said, "I've managed to keep them here until you arrived. They're ready."

"And what about you, Elizabeth?" Rodney asked not very tactfully. She hung her head and said "I think that I'll stay with you, if you'll let me. After all, this is pretty much my home."

John turned to the glowing forms. "Is this okay with you?" One of them- Lia- floated forward and said softly, "If this is her wish, then yes, we allow it. You (to Elizabeth) were the one that brought our feet onto the correct path." Elizabeth nodded and said "Congratulations, You have finally completed your predecessors' dream. Good luck in the next plane of existence."

Lia nodded. "We will always think of you, and perhaps we can help you in return, if you ever need it. But for now, farewell." The Asurans, all with faces of delight, became too bright to look at, and traveled up through the ceiling and vanished. The room went dark once again.

John let out a breath he didn't know he had been holding. Elizabeth turned again to them and said, with a certain amount of relief, "Well, it's finally over." Woolsey and McKay nodded vigorously in agreement. Sheppard must have made a face or something, because Elizabeth saw him, raised an eyebrow, and asked, "Something on your mind, John?"

John felt his face flush a little, and he covered it up by shrugging. "Well, this is sorta strange, right? You're back, ascended Replicators, creating humans… one hell of a week."

Woolsey laughed briefly. "You know, you're absolutely right Colonel. I suppose now that I was right when I said that the Pegasus Galaxy is weird like this." Most people in the room were nodding. He went on. "Well, it's late, and I feel like going to bed. Good night." And he left, Rodney following.

John also looked around. "He's right. I'm going to finish off my can of beer, and then I'm going to bed. Oh, by the way, Elizabeth… He looked at her awkwardly.

"Yes, John?"

"Thanks for coming back." And with that, John left for bed.

"No, Zelenka! The Zed.P.M needs to be powered by subspace, not a black hole!

"Yes, well, we can get unlimited energy from a black hole, unlike subspace, which is very, very limited. As you should well know, Rodney!

"Well, why don't you do it, then?"

"What- you little- how- tebe blbec! Tebe dát do oběhu debil! Tebe couldn't pochopit jeden chladně přijmout blaho idea -li ono brok tebe vzhledem k! Jak? člen určitý peklo did tebe stát se člen určitý hlava of tato fakulta? Kurva!"

John, walking in as Zelenka began his rant. He raised his eyebrows. "I think my Czech is almost fluent, because I understood all of that. I wouldn't repeat that to any kid. What's the big problem?"

McKay, having gone back to work rolled his eyes. "Mr. Clueless here thinks that we should power our Zed.P.M with energy from a black hole. That, of course, is impossible, as one: there are no black holes nearby, and two: we have no way of harnessing the energy."

Zelenka interrupted him. "Yes, but remember the Ori beach head? They powered the Supergate with a contained black hole! If we could set up a series of the Ancient satellites, the ones that have 

weapons, we could set up a system of power transfers that would end in the Zed.P.M. being continually powered. I made something similar back at home."

"That is _assuming_ we have enough of those satellites!"

"We could make small versions."

"Oh, sure, just build small Ancient satellites. Tell me when you find a way how, will you?"

"Kurva!"

During all this, Woolsey had come in unannounced, and walked over to them. "Colonel Sheppard, Doctor McKay, Doctor Zelenka. We have a bit of a situation on our hands."

All argument was postponed as all the people involved looked at the man in charge. "What sort of situation, sir?"

Woolsey's expression went sour. "One of our contacts on one planet has some rather bad news for us. Apparently, an old friend has shown his face again. Come with me.

Back in the Gate room, Sheppard and company, along with Woolsey and Elizabeth, gathered around a video monitor. Woolsey activated it, and a video started playing:

It was a rural village, normal in every way, but with some rather unwelcome changes. Walking along the main path, surrounded by Hybrids, was Michael.

A.N. Well, I hope that was a good chapter. Sorry to all you fans who wanted Elizabeth to get her old body back, but that plot line didn't seem complete somehow. I had to wrap up my ideas about Koracen, somehow. Plus, Michael is back now! What will happen… Can't wait until my next update! Bye!

Oh, bye the way, Zelenka's rant was in Czech. It wasn't really explicit; only a little.

Now, here are the responses I give to some reviews. I try to give as many answers as possible.

To Cocoa Girl: Um, I don't know. Maybe. As I hope you can see, I'm taking it slowly. Maybe later. Just be patient.

To The City of Atlantis: Thanks for having an open mind. You are in no danger from Michael.

To Alastria7: Hey, remember that they will have human bodies now. They can have emotions now. Plus, it's Fanfiction. I'm God here.

Now remember, review, or Replicators come after you. Lots of Mind probing. Bye!


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